Part of me thinks that Joe planted the rabbit head himself and was looking for a way to get rid of Len in order to gain Daryl's trust. He put Daryl in a no-lose situation. Why would Daryl ever admit to taking the rabbit if he didn't do it, and Joe clearly knew Daryl didn't do it so Daryl being a liar wasn't even tested.
I think we're going to, and have already seen, Daryl become more embedded with the group. It started with the blanket like you said, then the "claimed" strawberry. I think he's going to have to make choice between groups soon.